search

PHI-base / phi-eco

The PHI-base experimental conditions ontology
Other
1 stars 0 forks source link

Obsolete 'host assay in leaf' PECO:0005030 #9

Closed CuzickA closed 3 years ago

CuzickA commented 4 years ago

Val and I decided to capture this information using the AE BTO instead. https://github.com/PHI-base/curation/issues/19

CuzickA commented 3 years ago

This term has still not been obsoleted.

@jseager7 please could you see if this condition has been used in any curation sessions. Thanks.

jseager7 commented 3 years ago

Based on an export from 18 January, this term has only been used in PMID:16965554, but it's been used pretty extensively there. Seems like there are a few other obsolete phenotype terms and experimental conditions in the session.

CuzickA commented 3 years ago

Thanks.

It looks like this sessions needs some work.

Plan i) remove the 'host assay in leaf' condition from this session NEXT ii) reannotate session with metagenotype controls etc after I have finished reannotating the 10 sample papers required for the publication

CuzickA commented 3 years ago

I've now done i) remove the 'host assay in leaf' condition from this session

@jseager7 shall I obsolete the term via Protege?

jseager7 commented 3 years ago

@CuzickA Yes, I think obsoleting with Protege would be the best option.

To confirm it's worked, you should see this under the obsoleted term in the OBO file:

is_obsolete: true

Whereas in the OWL file, it should show something like this:

AnnotationAssertion(owl:deprecated obo:PECO_0005030 "true"^^xsd:boolean)
CuzickA commented 3 years ago

062dc88 term obsoleted